FMO DATABASE

FMODB ID: KR173

Calculation Name: 3DI3-A-Xray312

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

ligand 3-letter code: NAG

PDB ID: 3DI3

Chain ID: A

ChEMBL ID:

UniProt ID: P16871

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	120
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1042669.092946
FMO2-HF: Nuclear repulsion	992746.724627
FMO2-HF: Total energy	-49922.368319
FMO2-MP2: Total energy	-50062.411377

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:6:ACE )

Summations of interaction energy for fragment #1(A:6:ACE )

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-2.495	-0.955	1.529	-1.419	-1.65	0.002

Interaction energy analysis for fragmet #1(A:6:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.019

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	8	ASP	-1	-0.854	-0.926	3.852	-0.523	0.972	-0.005	-0.638	-0.851	-0.002
4	A	9	GLY	0	0.103	0.048	5.920	0.326	0.326	0.000	0.000	0.000	0.000
5	A	10	LYS	1	0.928	0.961	2.244	-3.200	-3.155	1.534	-0.781	-0.799	0.004
6	A	11	GLN	0	-0.010	-0.021	6.721	0.111	0.111	0.000	0.000	0.000	0.000
7	A	12	TYR	0	0.059	0.031	9.348	0.127	0.127	0.000	0.000	0.000	0.000
8	A	13	GLU	-1	-0.893	-0.950	10.191	-0.009	-0.009	0.000	0.000	0.000	0.000
9	A	14	SER	0	-0.023	-0.013	9.392	0.007	0.007	0.000	0.000	0.000	0.000
10	A	15	VAL	0	-0.024	-0.007	11.493	0.021	0.021	0.000	0.000	0.000	0.000
11	A	16	LEU	0	-0.027	0.001	13.968	0.060	0.060	0.000	0.000	0.000	0.000
12	A	17	MET	0	-0.033	-0.029	14.887	0.040	0.040	0.000	0.000	0.000	0.000
13	A	18	VAL	0	0.027	0.034	15.614	0.033	0.033	0.000	0.000	0.000	0.000
14	A	19	SER	0	-0.015	-0.034	18.179	0.015	0.015	0.000	0.000	0.000	0.000
15	A	20	ILE	0	-0.034	-0.018	18.330	0.018	0.018	0.000	0.000	0.000	0.000
16	A	21	ASP	-1	-0.803	-0.903	19.266	-0.076	-0.076	0.000	0.000	0.000	0.000
17	A	22	GLN	0	-0.013	0.005	22.288	0.020	0.020	0.000	0.000	0.000	0.000
18	A	23	LEU	0	-0.041	-0.012	24.387	0.009	0.009	0.000	0.000	0.000	0.000
19	A	24	LEU	0	-0.015	-0.002	23.445	0.011	0.011	0.000	0.000	0.000	0.000
20	A	25	ASP	-1	-0.839	-0.917	25.926	-0.045	-0.045	0.000	0.000	0.000	0.000
21	A	26	SER	0	-0.077	-0.044	28.072	0.006	0.006	0.000	0.000	0.000	0.000
22	A	27	MET	0	-0.039	-0.021	28.954	0.005	0.005	0.000	0.000	0.000	0.000
23	A	28	LYS	1	0.854	0.929	28.504	0.044	0.044	0.000	0.000	0.000	0.000
24	A	29	GLU	-1	-0.899	-0.951	32.055	-0.023	-0.023	0.000	0.000	0.000	0.000
25	A	30	ILE	0	-0.051	-0.005	33.768	0.002	0.002	0.000	0.000	0.000	0.000
26	A	31	GLY	0	0.006	-0.036	34.595	0.001	0.001	0.000	0.000	0.000	0.000
27	A	32	SER	0	-0.007	-0.014	36.460	0.000	0.000	0.000	0.000	0.000	0.000
28	A	33	ASN	0	0.025	-0.001	39.522	0.001	0.001	0.000	0.000	0.000	0.000
29	A	129	CYS	0	0.004	0.038	33.219	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	35	LEU	0	0.029	0.037	35.692	0.000	0.000	0.000	0.000	0.000	0.000
31	A	36	ASN	0	-0.027	-0.003	35.171	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	37	ASN	0	-0.007	-0.020	37.297	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	38	GLU	-1	-0.890	-0.917	35.890	-0.017	-0.017	0.000	0.000	0.000	0.000
34	A	39	PHE	0	0.046	0.013	35.034	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	40	ASN	0	0.016	-0.016	35.741	0.001	0.001	0.000	0.000	0.000	0.000
36	A	41	PHE	0	-0.060	-0.032	28.398	0.001	0.001	0.000	0.000	0.000	0.000
37	A	42	PHE	0	0.051	0.022	28.702	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	43	LYS	1	0.914	0.982	31.983	0.018	0.018	0.000	0.000	0.000	0.000
39	A	44	ARG	1	0.903	0.932	33.866	0.028	0.028	0.000	0.000	0.000	0.000
40	A	45	HIS	0	-0.026	-0.016	28.747	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	46	ILE	0	0.099	0.051	27.883	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	141	CYS	0	-0.083	-0.022	18.650	0.004	0.004	0.000	0.000	0.000	0.000
43	A	48	ASP	-1	-0.836	-0.927	24.560	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	49	ALA	0	-0.035	-0.030	22.037	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	50	ASN	0	0.003	0.019	22.177	0.004	0.004	0.000	0.000	0.000	0.000
46	A	51	LYS	1	0.933	0.971	21.162	0.056	0.056	0.000	0.000	0.000	0.000
47	A	52	GLU	-1	-0.692	-0.852	19.227	-0.015	-0.015	0.000	0.000	0.000	0.000
48	A	53	GLY	0	0.058	0.012	19.721	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	54	MET	0	-0.135	-0.077	20.318	-0.015	-0.015	0.000	0.000	0.000	0.000
50	A	55	PHE	0	0.051	0.034	22.711	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	56	LEU	0	0.059	0.032	18.217	0.001	0.001	0.000	0.000	0.000	0.000
52	A	57	PHE	0	0.028	0.020	21.969	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	58	ARG	1	0.893	0.945	23.490	0.058	0.058	0.000	0.000	0.000	0.000
54	A	59	ALA	0	0.019	0.000	24.087	0.000	0.000	0.000	0.000	0.000	0.000
55	A	60	ALA	0	0.034	0.031	22.654	0.000	0.000	0.000	0.000	0.000	0.000
56	A	61	ARG	1	0.855	0.918	24.200	0.116	0.116	0.000	0.000	0.000	0.000
57	A	62	LYS	1	0.898	0.961	27.955	0.058	0.058	0.000	0.000	0.000	0.000
58	A	63	LEU	0	0.070	0.039	24.195	0.006	0.006	0.000	0.000	0.000	0.000
59	A	64	ARG	1	0.914	0.969	26.926	0.111	0.111	0.000	0.000	0.000	0.000
60	A	65	GLN	0	-0.046	-0.018	29.923	0.003	0.003	0.000	0.000	0.000	0.000
61	A	66	PHE	0	0.008	0.009	31.365	0.006	0.006	0.000	0.000	0.000	0.000
62	A	67	LEU	0	0.009	0.015	28.989	0.001	0.001	0.000	0.000	0.000	0.000
63	A	68	LYS	1	0.945	0.974	33.177	0.060	0.060	0.000	0.000	0.000	0.000
64	A	69	MET	0	-0.017	0.008	36.354	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	70	ASN	0	-0.034	-0.033	33.953	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	71	SER	0	0.021	0.020	34.691	0.000	0.000	0.000	0.000	0.000	0.000
67	A	72	THR	0	0.021	-0.024	32.117	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	73	GLY	0	0.027	0.054	32.112	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	74	ASP	-1	-0.853	-0.945	27.824	-0.095	-0.095	0.000	0.000	0.000	0.000
70	A	75	PHE	0	-0.014	-0.011	27.536	-0.009	-0.009	0.000	0.000	0.000	0.000
71	A	76	ASP	-1	-0.857	-0.946	28.353	-0.082	-0.082	0.000	0.000	0.000	0.000
72	A	77	LEU	0	0.032	0.020	26.083	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	78	HIS	0	0.038	0.029	22.463	-0.026	-0.026	0.000	0.000	0.000	0.000
74	A	79	LEU	0	0.010	0.013	23.590	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	80	LEU	0	-0.008	-0.004	24.858	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	81	LYS	1	0.989	0.999	20.312	0.166	0.166	0.000	0.000	0.000	0.000
77	A	82	VAL	0	0.037	0.031	20.063	-0.021	-0.021	0.000	0.000	0.000	0.000
78	A	83	SER	0	-0.051	-0.020	20.602	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	84	GLU	-1	-0.945	-0.969	21.267	-0.166	-0.166	0.000	0.000	0.000	0.000
80	A	85	GLY	0	0.077	0.023	17.992	-0.018	-0.018	0.000	0.000	0.000	0.000
81	A	86	THR	0	-0.009	-0.030	16.981	-0.032	-0.032	0.000	0.000	0.000	0.000
82	A	87	THR	0	-0.117	-0.078	18.308	0.013	0.013	0.000	0.000	0.000	0.000
83	A	88	ILE	0	-0.026	-0.011	16.127	0.004	0.004	0.000	0.000	0.000	0.000
84	A	89	LEU	0	-0.005	0.013	10.990	-0.031	-0.031	0.000	0.000	0.000	0.000
85	A	90	LEU	0	-0.018	0.025	14.036	0.001	0.001	0.000	0.000	0.000	0.000
86	A	91	ASN	0	0.021	0.007	16.289	0.017	0.017	0.000	0.000	0.000	0.000
87	A	92	CYS	0	-0.055	-0.028	12.471	0.025	0.025	0.000	0.000	0.000	0.000
88	A	93	THR	0	-0.031	-0.041	10.516	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	94	GLY	0	0.063	0.042	12.776	0.057	0.057	0.000	0.000	0.000	0.000
90	A	95	GLN	0	-0.102	-0.050	15.481	0.034	0.034	0.000	0.000	0.000	0.000
91	A	96	VAL	0	0.027	0.009	18.579	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	97	LYS	1	0.853	0.933	21.215	0.091	0.091	0.000	0.000	0.000	0.000
93	A	98	GLY	0	0.065	0.028	24.634	-0.012	-0.012	0.000	0.000	0.000	0.000
94	A	99	NME	0	0.016	0.024	27.301	0.007	0.007	0.000	0.000	0.000	0.000
95	A	121	ACE	0	0.055	0.019	37.459	0.000	0.000	0.000	0.000	0.000	0.000
96	A	122	GLN	0	-0.050	-0.033	31.861	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	123	LYS	1	0.949	0.977	37.281	0.042	0.042	0.000	0.000	0.000	0.000
98	A	124	LYS	1	0.967	0.977	36.302	0.055	0.055	0.000	0.000	0.000	0.000
99	A	125	LEU	0	-0.043	-0.022	33.494	0.004	0.004	0.000	0.000	0.000	0.000
100	A	126	ASN	0	0.000	-0.018	36.348	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	127	ASP	-1	-0.833	-0.924	36.909	-0.035	-0.035	0.000	0.000	0.000	0.000
102	A	128	LEU	0	0.087	0.028	33.211	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	130	PHE	0	-0.036	-0.013	31.261	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	131	LEU	0	0.003	-0.006	28.654	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	132	LYS	1	0.971	1.004	28.720	0.027	0.027	0.000	0.000	0.000	0.000
106	A	133	ARG	1	0.954	0.988	27.924	0.023	0.023	0.000	0.000	0.000	0.000
107	A	134	LEU	0	-0.079	-0.038	26.872	0.000	0.000	0.000	0.000	0.000	0.000
108	A	135	LEU	0	0.028	-0.004	23.942	-0.006	-0.006	0.000	0.000	0.000	0.000
109	A	136	GLN	0	0.003	0.007	23.264	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	137	GLU	-1	-0.860	-0.935	22.954	-0.031	-0.031	0.000	0.000	0.000	0.000
111	A	138	ILE	0	-0.055	-0.036	20.326	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	139	LYS	1	0.837	0.926	18.771	0.049	0.049	0.000	0.000	0.000	0.000
113	A	140	THR	0	0.005	-0.005	18.393	0.000	0.000	0.000	0.000	0.000	0.000
114	A	142	TRP	0	0.006	0.005	13.974	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	143	ASN	0	0.038	0.009	13.754	0.005	0.005	0.000	0.000	0.000	0.000
116	A	144	LYS	1	0.861	0.944	14.757	0.032	0.032	0.000	0.000	0.000	0.000
117	A	145	ILE	0	-0.061	-0.029	14.395	0.014	0.014	0.000	0.000	0.000	0.000
118	A	146	LEU	0	-0.062	-0.023	9.538	-0.011	-0.011	0.000	0.000	0.000	0.000
119	A	147	MET	0	-0.086	-0.050	10.479	0.075	0.075	0.000	0.000	0.000	0.000
120	A	148	NME	0	0.018	0.031	13.322	-0.005	-0.005	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:6:ACE )